Polypeptide backbone NMR chemical shifts are proven powerful descriptors of local dynamic deviations from the "random coil" state toward canonical types of secondary structure. These digressions, in turn, can be connected to functional or dysfunctional protein states, for example, in adaptive molecular recognition and protein aggregation.
The ncIDP tool makes use of backbone (15)N, (1)H(N), (1)H(α), (13)C(O), (13)C(β), and (13)C(α) chemical shifts derived from a set of 14 intrinsically disordered proteins of unrelated sequence and function. The ncIDP prediction accuracy is significantly higher than that obtained with libraries for small peptides or "coil" regions of folded proteins.
I strongly recommend selecting a decent cloud-based storage and installing the app on an Nginx-powered server.
I have personally followed this setup guide, and it worked like a charm: https://www.digitalocean.com/community/tutorials/how-to-deploy-a-meteor-js-application-on-ubuntu-14-04-with-nginx
- Select random coil NMR chemical shift library.
- Provide a FASTA-formatted protein sequence.
- Download or send via email the predicted chemical shift table.
- Fork it!
- Create your feature branch:
git checkout -b my-new-feature - Commit your changes:
git commit -am 'Add some feature' - Push to the branch:
git push origin my-new-feature - Submit a pull request :D
Current release: 1.0a
Developed and programmed by Kamil Tamiola (https://www.tamiola.com) and Frans A. A. Mulder (http://nmr.au.dk/).
Based on the doctoral research and PhD dissertation of Kamil Tamiola, NMR & Molecular Dynamics Group at University of Groningen, the Netherlands.
If you intend to use, or modify the tool, please cite in your scientific work the following source:
Tamiola, K., Acar, B. & Mulder, F. A. A. Sequence-specific random coil chemical shifts of intrinsically disordered proteins. J. Am. Chem. Soc. 132, 18000–18003 (2010). http://pubs.acs.org/doi/abs/10.1021/ja105656t
Copyright (c) 2015 Kamil Tamiola
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